Bacterial genome chimaerism and the origin of mitochondria

Canadian Journal of Microbiology

Volumn 57, Issue 1, 2011, Pages 49-61

  Abhishek, Ankur ^a   Bavishi, Anish ^a   Bavishi, Ashay ^a   Choudhary, Madhusudan ^a  

^a Sam Houston State University   (United States)

Author keywords

Alphaproteobacteria; Endosymbiotic theory; Mitochondria origin

Indexed keywords

ALPHAPROTEOBACTERIA; BACTERIAL GENOMES; EN-ROUTE; ENDOSYMBIOTIC THEORY; MITOCHONDRIAL GENES; MITOCHONDRIAL PROTEIN; OCHROBACTRUM ANTHROPI; PHYLOGENETIC ANALYSIS; RHODOBACTER SPHAEROIDES; RHODOPSEUDOMONAS PALUSTRIS; RHODOSPIRILLUM RUBRUM; SACCHAROMYCES CEREVISIAE; SEQUENCE SIMILARITY;

BACTERIOLOGY; GENES; YEAST;

MITOCHONDRIA;

MITOCHONDRIAL PROTEIN;

BACTERIUM; GENOME; MITOCHONDRION; PHYLOGENETICS; PROTEIN; YEAST;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; CHIMERA; CONTROLLED STUDY; DNA BASE COMPOSITION; GENOME SIZE; MITOCHONDRIAL GENE; MITOCHONDRION; NONHUMAN; OCHROBACTRUM ANTHROPI; PHYLOGENY; PLASMID; PRIORITY JOURNAL; RHODOBACTER SPHAEROIDES; RHODOPSEUDOMONAS PALUSTRIS; RHODOSPIRILLUM RUBRUM; RICKETTSIA PROWAZEKII; SACCHAROMYCES CEREVISIAE; SCORING SYSTEM; SEQUENCE ANALYSIS; SISTER GROUP;

ALPHAPROTEOBACTERIA; BIOLOGICAL EVOLUTION; EUKARYOTA; GENOME, BACTERIAL; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; PHYLOGENY; SACCHAROMYCES CEREVISIAE;

ALPHAPROTEOBACTERIA; ANAPLASMATACEAE; BACTERIA (MICROORGANISMS); OCHROBACTRUM ANTHROPI; RECLINOMONAS AMERICANA; RHODOBACTER SPHAEROIDES; RHODOPSEUDOMONAS PALUSTRIS; RHODOSPIRILLACEAE; RHODOSPIRILLUM RUBRUM; RICKETTSIA PROWAZEKII; RICKETTSIACEAE; RICKETTSIALES; SACCHAROMYCES CEREVISIAE;

EID: 79953125998     PISSN: 00084166     EISSN: 14803275     Source Type: Journal    
DOI: 10.1139/W10-099     Document Type: Article

References (37)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17): 3389-3402. doi:10.1093/nar/25.17. 3389. PMID:9254694.
2. Andersson, S.G., Zomorodipour, A., Andersson, J.O., Sicheritz-Pontén, T., Alsmark, U.C., Podowski, R.M., et al. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature (Lond.), 396(6707): 133-140. doi:10.1038/24094. PMID:9823893.
3. Andersson, S.G., Karlberg, O., Canbäck, B., and Kurland, C.G. 2003. On the origin of mitochondria: a genomics perspective. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358(1429): 165-179. doi:10.1098/rstb.2002.1193. PMID:12594925.
4. Atteia, A., Adrait, A., Brugière, S., Tardif, M., van Lis, R., Deusch, O., et al. 2009. A proteomic survey of Chlamydomonas rein-hardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the α-proteobacterial mito-chondrial ancestor. Mol. Biol. Evol. 26(7): 1533-1548. doi:10. 1093/molbev/msp068. PMID:19349646.
5. Battistuzzi, F.U., Feijao, A., and Hedges, S.B. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4(1): 44. doi:10.1186/1471-2148-4-44. PMID: 15535883.
6. Bergthorsson, U., Adams, K.L., Thomason, B., and Palmer, J.D. 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature (Lond.), 424(6945): 197-201. doi:10. 1038/nature01743. PMID:12853958.
7. Chose, O., Sarde, C.O., Gerbod, D., Viscogliosi, E., and Roseto, A. 2003a. Programmed cell death in parasitic protozoans that lack mitochondria. Trends Parasitol. 19(12): 559-564. doi:10.1016/j. pt.2003.09.016. PMID:14642765.
8. Chose, O., Sarde, C.O., Noël, C., Gerbod, D., Jimenez, J.C., Brenner, C., et al. 2003b. Cell death in protists without mitochondria. Ann. N. Y. Acad. Sci. 1010(1): 121-125. doi:10.1196/annals. 1299.021. PMID:15033707.
9. Drummond, A., Ashton, B., Buxton, S., Cheung, M., Heled, J., Kearse, M., et al. 2010. Geneious, version 4.8. Available from http://www.geneious.com [accessed 17 June 2009].
10. Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5): 1792-1797. doi:10.1093/nar/gkh340. PMID:15034147.
11. Embley, T.M., and Martin, W. 2006. Eukaryotic evolution, changes and challenges. Nature (Lond.), 440(7084): 623-630. doi:10. 1038/nature04546. PMID:16572163.
12. Emelyanov, V.V. 2001. Rickettsiaceae, Rickettsia-like endosym-bionts, and the origin of mitochondria. Biosci. Rep. 21(1): 1-17. doi:10.1023/A:1010409415723. PMID:11508688.
13. Esser, C., Ahmadinejad, N., Wiegand, C., Rotte, C., Sebastiani, F., Gelius-Dietrich, G., et al. 2004. A genome phylogeny for mitochondria among a-proteobacteria and a predominantly eubacter-ial ancestry of yeast nuclear genes. Mol. Biol. Evol. 21(9): 1643-1660. doi:10.1093/molbev/msh160. PMID:15155797.
14. Esser, C., Martin, W., and Dagan, T. 2007. The origin of mitochondria in light of a fluid prokaryotic chromosome model. Biol. Lett. 3(2): 180-184. doi:10.1098/rsbl.2006.0582. PMID: 17251118.
15. Feng, D.F., Cho, G., and Doolittle, R.F. 1997. Determining divergence times with a protein clock: update and reevaluation. Proc. Natl. Acad. Sci. U.S.A. 94(24): 13028-13033. doi:10.1073/pnas. 94.24.13028. PMID:9371794.
16. Fitzpatrick, D.A., Creevey, C.J., and McInerney, J.O. 2006. Genome phylogenies indicate a meaningful a-proteobacterial phylo-geny and support a grouping of the mitochondria with the Rickettsiales. Mol. Biol. Evol. 23(1): 74-85. doi:10.1093/molbev/msj009. PMID:16151187.
17. Giovannoni, S.J., Tripp, H.J., Givan, S., Podar, M., Vergin, K.L., Baptista, D., et al. 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science, 309(5738): 1242-1245. doi:10. 1126/science.1114057. PMID:16109880.
18. Gray, M.W., Burger, G., and Lang, B.F. 1999. Mitochondrial evolution. Science, 283(5407): 1476-1481. doi:10.1126/science.283. 5407.1476. PMID:10066161.
19. Guindon, S., and Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52(5): 696-704. doi:10.1080/10635150390235520. PMID:14530136.
20. Hazkani-Covo, E., Zeller, R.M., Martin, W., and Malik, H.S. 2010. Molecular poltergeists: mitochondrial DNA copies (numts) in se-quenced nuclear genomes. PLoS Genet. 6(2): e1000834. doi:10. 1371/journal.pgen.1000834. PMID:20168995.
21. Henriquez, F.L., Richards, T.A., Roberts, F., McLeod, R., and Roberts, C.W. 2005. The unusual mitochondrial compartment of Cryptosporidium parvum. Trends Parasitol. 21(2): 68-74. doi:10.1016/j.pt.2004.11.010. PMID:15664529.
22. Imhoff, J.F., and Trüper, H.G. 1992. The genus Rhodospirillum and related genera. In The prokaryotes. Edited by A. Balows, H.G. Trüper, M. Dworkin, W. Harder, and K.-H. Schleifer. SpringerVerlag, New York. pp. 2141-2159.
23. Javaux, E.J., Knoll, A.H., and Walter, M.R. 2001. Morphological and ecological complexity in early eukaryotic ecosystems. Nature (Lond.), 412(6842): 66-69. doi:10.1038/35083562. PMID: 11452306.
24. Karlberg, O., Canbäck, B., Kurland, C.G., and Andersson, S.G. 2000. The dual origin of the yeast mitochondrial proteome. Yeast, 17(3): 170-187. doi:10.1002/1097-0061(20000930) 17:3<170::AID-YEA25>3.0.CO;2-V. PMID:11025528.
25. Kersters, K., Devos, P., Gillis, M., Swings, J., Vandamme, P., and Stackebrandt, E. 2006. Introduction to the proteobacteria. In The prokaryotes: a handbook on the biology of bacteria. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.H. Schleifer, and E. Stackebrandt. Springer-Verlag, New York. pp. 3-37.
26. Lang, B.F., Burger, G., O'Kelly, C.J., Cedergren, R., Golding, G.B., Lemieux, C., et al. 1997. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature (Lond.), 387(6632): 493-497. doi:10.1038/387493a0. PMID: 9168110.
27. Lang, B.F., Gray, M.W., and Burger, G. 1999a. Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet. 33(1): 351-397. doi:10.1146/annurev.genet.33.1.351. PMID: 10690412.
28. Lang, B.F., Seif, E., Gray, M.W., O'Kelly, C.J., and Burger, G. 1999b. A comparative genomics approach to the evolution of eukaryotes and their mitochondria. J. Eukaryot. Microbiol. 46(4): 320-326. doi:10.1111/j.1550-7408.1999.tb04611.x. PMID:10461380.
29. Plasterer, T.N., Smith, T.F., and Mohr, S.C. 2001. Survey of human mitochondrial diseases using new genomic/proteomic tools. Genome Biol. 2(6): research0021.1-research0021.16. doi:10. 1186/gb-2001-2-6-research0021. PMID:11423010.
30. Pollock, D.D., Zwickl, D.J., McGuire, J.A., and Hillis, D.M. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51(4): 664-671. doi:10.1080/10635150290102357. PMID:12228008.
31. Rosenberg, M.S., and Kumar, S. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. U.S.A. 98(19): 10751-10756. doi:10.1073/pnas.191248498. PMID:11526218.
32. Rosenberg, M.S., and Kumar, S. 2003. Taxon sampling, bioinfor-matics, and phylogenomics. Syst. Biol. 52(1): 119-124. doi:10. 1080/10635150390132894. PMID:12554445.
33. Timmis, J.N., Ayliffe, M.A., Huang, C.Y., and Martin, W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryo-tic chromosomes. Nat. Rev. Genet. 5(2): 123-135. doi:10.1038/nrg1271. PMID:14735123.
34. Whelan, S., and Goldman, N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18(5): 691-699. PMID:11319253.
35. Williams, K.P., Sobral, B.W., and Dickerman, A.W. 2007. A robust species tree for the Alphaproteobacteria. J. Bacteriol. 189(13): 4578-4586. doi:10.1128/JB.00269-07. PMID:17483224.
36. Wu, M., Sun, L.V., Vamathevan, J., Riegler, M., Deboy, R., Brownlie, J.C., et al. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2(3): e69. doi:10. 1371/journal.pbio.0020069. PMID:15024419.
37. Zwickl, D.J., and Hillis, D.M. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51(4): 588-598. doi:10.1080/10635150290102339. PMID:12228001.